HELANAL: A program to characterize overall geometry of an alpha helix Sandeep Kumar and Manju Bansal, Molecular Biophysics Unit, India Institute of Science, Bangalore - 560012, INDIA. Brief description of HELANAL The program can be used to characterize the geometry of helices with a minimum 9 residues. Geometry of an alpha helix is characterised by computing local helix axes and local helix origins for four contiguous C-Alpha atoms, using the procedure of Sugeta and Miyazawa,1967 (Sugeta, H. & Miyazawa, T. 1967. General method for calculating helical parameters of polymer chains from bond lengths, bond angles and internal- rotation angles. Biopolymers 5, 673 - 679.) and sliding this window over the length of the helix in steps of one C-Alpha atom. The angles between successive local helix axes can identify local bends or kinks as well as occurrence of smooth curvature in the helix. A matrix, whose elements M(I, J) are the bending angles between local helix axes I and J, is obtained to get an idea about the overall geometry of the helix. Unit twist and unit height of the alpha helix are also computed to analyse the uniformity of the helix. The local helix origins trace out the path described by the helix in three dimensional space. The local helix origins are reoriented in X-Y plane and the reoriented points are used to fit a circle as well as a line, by least squares method. To know more about HELANAL, its algorithm and potential applications, please refer to: Kumar, S. and Bansal, M. 1996. Structural and sequence characteristics of long alpha-helices in globular proteins. Biophysical Journal, 71, 3, 1574-1586. Kumar, S. and Bansal, M. 1998. Geometrical and sequence characteristics of alpha helices in globular proteins. Biophysical Journal, 75, 4, 1935-1944. Bansal, M., Kumar, S. and Velavan, R. 2000. HELANAL - A program to characterise helix geometry in proteins. Journal of Biomolecular Structure and Dynamics, 17, 5, 811 - 819. Compiling HELANAL HELANAL is coded in FORTRAN 77. It has been successfully compiled using several FORTRAN compilers, on IBM RS-6000, SUN-SPARC and Silicon Graphics workstations, under UNIX environment. It has also been compiled on IBM-PC compatible machines running in UNIX/LINUX environment as well as in DOS. Some linux compilers may give problem with the Max function in this program. In those cases, just rename the Max function of helanal. INPUT to HELANAL Input files to this program can be different depending upon the options chosen. The program can directly read HELIX records in one or more PDB files. In order to analyse helices found in helix records of a PDB file, give the PDB file name as input to the program. In order to analyse the helices found in the HELIX records of a large number of PDB files, the a file containing the PDB files names in format (5x, a11) can be used to provide input to the program. HELIX records in PDB files vary with the definition used for alpha helix by different laboratories. Therefore provision is also made to read the information about helix start/end residues through a file (e.g. hel.inp). In case the helix records in this file are in a different format from that of PDB, the format of the input file is also an input to the program. Finally files other than PDB files (or the files containing coordinates of C-alpha atoms in the PDB format) can also be given as input to HELANAL after specifying their formats. The input coordinate file(s) should be in the same directory as the other input files, if any. In case the PDB files contain alternate (more than one) C-Alpha atom positions, for any amino acid residue, use only one of the two C-Alpha positions when running HELANAL. OUTPUT FILES from HELANAL For each run of HELANAL the following output files are created. RUN.ANS contains the questions and their answers during a run of HELANAL. HELCA.OUT contains Coordinates of the C-alpha atoms. HELINFO.OUT file is created only when the HELIX records in the PDB files are used for information on helix start/end residues and contains these helix records. AXES.OUT contains the local helix axes fitted to 4 consecutive C-alpha atoms along with a matrix M(I, J) whose elements are the angles between local helix axes I and J. ANGLE.OUT contains the angle between successive local helix axes. It also gives mean bending angle and Maximum bending angle for the helix. ORIGIN.OUT contains the local helix origins for the helix along with statistics obtained by fitting least square plane, circle and line to the local helix origins. NH.OUT contains unit height and unit twist for every turn of the helix as well as average unit height and average unit twist for the whole helix. ***.PRM contains summary of various parameters obtained by HELANAL. ***.TAB presents the results in tabular form along with the overall geometry assignment for the helices. BUGS/TROUBLE SHOOTING IF you face any problem/find any bugs in the program, please report to the authors by sending email(s) at the following addresses: kumarsan@ncifcrf.gov mb@mbu.iisc.ernet.in Please cite one or more of the following references if you use the program: Bansal, M., Kumar, S. and Velavan, R. 2000. HELANAL - A program to characterise helix geometry in proteins. Journal of Biomolecular Structure and Dynamics, 17, 5, 811 - 819. Kumar, S. and Bansal, M. 1996. Structural and sequence characteristics of long alpha-helices in globular proteins. Biophysical Journal, 71, 3, 1574-1586. Kumar, S. and Bansal, M. 1998. Geometrical and sequence characteristics of alpha helices in globular proteins. Biophysical Journal, 75, 4, 1935-1944. CONTENTS This package contains the following files: source codes for: helanal.f : The HELANAL Program Sample I/O files.